MANTiS neonate tissue segmentation

Preliminaries

MANTiS is designed to process brain extracted T2 weighted images that are in the same orientation
as the template. Orientation in this case doesn’t imply that the new image and template
should be registered - simply that the data ordering is the same. We use the fslswapdim tool
to control data ordering.

All scans processed in a single batch must be in the same folder!

Brain extraction for the MANTiS validation studies were carried out using FSL BET. There
is also a preliminary tool in MANTiS to perform brain extraction.

Finally, as with typical SPM segmentation, the origins of the image need to be roughly equivalent
to the template. There is a tool in MANTiS to set the origin based on the centre of mass. This
tool should also be applied to brain extracted images.

Getting started

MANTiS is an SPM toolbox and can be accessed as follows.

Select mantis from the toolbox dropdown menu:

Select the complete pipeline option to load the pipeline in the batch editor.

Brain Extraction

Setting image origin

SPM segmentation utilises the image origin from the nifti files if it
is set on the assumption that is positioned similarly to the origin of
standard space. Strange results can occur if this isn’t the
case. A tool for setting image origin: based on the centre
of mass of the brain is available. It should be applied to brain
extracted images.

Preprocessing pipeline

A pipeline performing brain extraction and origin setting can be
constructed in the batch editor as per the image below:

Make sure that the input volumes for the “Origin to COM” tool are set using the Dependency button and select Simple watershed scalping: scalped structurals from the options.

Check the output images for successful scalping, then feed into MANTiS tissue classification.

Changing templates

The template image used by mantis is specified in a defaults file: mantis/cg_mantis_defaults.m
A custom template can be used by changing the mantis.opts.tpm and mantis.opts.tpm2
variables in this file to reference your own template. The components
of the custom template must match those in the original (at least for
gray, white and csf tissue classes), and changes will affect all
toolbox users. Use multiple copies of the toolbox to simultaneously
test different templates.